esys-escript

How do I compile escript v5.1 on RHEL 6.9?

Asked by Robert Vestandig

We run RHEL 6.9 cluster nodes here and so far I have not been able to compile using the Centos 7 template. Which template do I need?

Also the netcdf-cxx-devel doesn't appear to exist anywhere. Will missing this be a problem?

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Joel Fenwick (j-fenwick1) said : 		#1

Netcdf will not be a problem provided you don't need to be able to save or load from netcdf files (Just set your netcdf variable to False in the options file).

Can you give me some indication of what libraries are causing problems on 6.9?

Revision history for this message
Robert Vestandig (rverstandig) said : 		#2

Hi Joel

I've also attached the config.log file for both build attempts. I'm sure this is just a template issue but I am not that familiar with this stuff..

######################################################################################
On Build 5.1 I get the following errors:

# scons -j1 options_file=scons/templates/centos7_0_options.py
scons: Reading SConscript files ...
Using options in scons/templates/centos7_0_options.py.
Checking whether the C++ compiler worksno
Cannot run C++ compiler 'g++' (check config.log)

######################################################################################
On Build 4.2 I get the following errors:

escriptcore/src/SubWorld.cpp: In member function 'bool escript::SubWorld::localTransport(std::string&)':
escriptcore/src/SubWorld.cpp:244: error: 'class boost::python::api::object' has no member named 'is_none'
escriptcore/src/SubWorld.cpp: In member function 'char escript::SubWorld::runJobs(std::string&)':
escriptcore/src/SubWorld.cpp:976: error: 'class boost::python::api::object' has no member named 'is_none'
scons: *** [build/posix/escriptcore/SubWorld.os] Error 1
scons: building terminated because of errors.

*** Config Summary (see config.log and <prefix>/lib/buildvars for details) ***
Escript/Finley revision -2
  Install prefix: /share/data/apps/escript/4.2
          Python: /usr
           boost: /usr (Version 1.41.0)
           numpy: YES (with headers)
             MPI: NO
        ParMETIS: NO
          LAPACK: NO
            CUDA: NO
          openmp: YES
          netcdf: YES
           scipy: YES
           debug: NO
       boomeramg: NO
         cppunit: NO
            gdal: NO
             mkl: NO
            papi: NO
          pyproj: NO
            silo: NO
           sympy: NO
         umfpack: NO
           visit: NO
            gmsh: YES
            gzip: NO
  Treating warnings as errors

WARNING: Cannot import pyproj. Inversions may not work.
WARNING: Cannot import gdal. Inversions will not honour WKT coordinate system information.
WARNING: Cannot import sympy. Symbolic toolbox and nonlinear PDEs will not be available.

ERROR: build stopped due to errors

######################################################################################

Robert W Verstandig  |  Senior Technologist, Exploration Geophysics
Western Australian School of Mines: Minerals, Energy and Chemical Engineering
Faculty of Science and Engineering

[Postal Address:  GPO Box U1987, Perth, Western Australia, 6845]   [Bld 613, Rm 409]
[Street Address:  ARRC/CSIRO Building, H Block Level 4, 26 Dick Perry Avenue, Kensington 6151, Western Australia]

Tel     | +61 8 9266 4975
Fax    | +61 8 9266 3407
Email | <email address hidden>
Web   | www.geophysics.curtin.edu.au

Curtin University is a trademark of Curtin University of Technology
CRICOS Provider Code 00301J (WA)

-----Original Message-----
From: <email address hidden> <email address hidden> On Behalf Of Joel Fenwick
Sent: Tuesday, 20 March 2018 12:14 PM
To: Robert Verstandig <email address hidden>
Subject: Re: [Question #666736]: How do I compile escript v5.1 on RHEL 6.9?

Your question #666736 on esys-escript changed:
https://answers.launchpad.net/escript-finley/+question/666736

    Status: Open => Needs information

Joel Fenwick requested more information:
Netcdf will not be a problem provided you don't need to be able to save or load from netcdf files (Just set your netcdf variable to False in the options file).

Can you give me some indication of what libraries are causing problems on 6.9?

--
To answer this request for more information, you can either reply to this email or enter your reply at the following page:
https://answers.launchpad.net/escript-finley/+question/666736

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Revision history for this message
Robert Vestandig (rverstandig) said : 		#3

Hi Joel

Seems our compiler is too old to compile the latest release but there looks like there may be a solution with a complier flags adjustment.

Apparently the compiler we have, gcc 4.4.1, supports the "-std=gnu++0x" flag. Changing the compiler flag from "-std=c++11" to "-std=gnu++0x" successfully compiles the test script.

Where do I make this change in the actual full recompile though and if I do this would it have any bad side effects?

Cheers

Robert W Verstandig  |  Senior Technologist,  Exploration Geophysics
Western Australian School of Mines: Minerals, Energy and Chemical Engineering
Faculty of Science and Engineering

[Postal Address:  GPO Box U1987, Perth, Western Australia, 6845]   [Bld 613, Rm 409]
[Street Address:  ARRC/CSIRO Building, H Block Level 4, 26 Dick Perry Avenue, Kensington 6151, Western Australia]

Tel     | +61 8 9266 4975
Fax    | +61 8 9266 3407
Email | <email address hidden>
Web   | www.geophysics.curtin.edu.au

Curtin University is a trademark of Curtin University of Technology
CRICOS Provider Code 00301J (WA)

-----Original Message-----
From: <email address hidden> <email address hidden> On Behalf Of Joel Fenwick
Sent: Tuesday, 20 March 2018 12:14 PM
To: Robert Verstandig <email address hidden>
Subject: Re: [Question #666736]: How do I compile escript v5.1 on RHEL 6.9?

Your question #666736 on esys-escript changed:
https://answers.launchpad.net/escript-finley/+question/666736

    Status: Open => Needs information

Joel Fenwick requested more information:
Netcdf will not be a problem provided you don't need to be able to save or load from netcdf files (Just set your netcdf variable to False in the options file).

Can you give me some indication of what libraries are causing problems on 6.9?

--
To answer this request for more information, you can either reply to this email or enter your reply at the following page:
https://answers.launchpad.net/escript-finley/+question/666736

You received this question notification because you asked the question.

Revision history for this message
Joel Fenwick (j-fenwick1) said : 		#4

I added the following to my options file:

cc_flags = "-std=gnu++0x -pedantic -Wall -fPIC -Wno-unknown-pragmas -Wno-sign-compare -Wno-system-headers -Wno-long-long -Wno-strict-aliasing -finline-functions"

(It's just the default values with that flag switched.)

I did a build like that and it passed all tests (on my non-RHEL system) so give it a go.

Revision history for this message
Robert Vestandig (rverstandig) said : 		#5

Excellent!

Thanks Joel, I will give it a try.

Robert W Verstandig  |  Senior Technologist,  Exploration Geophysics
Western Australian School of Mines: Minerals, Energy and Chemical Engineering
Faculty of Science and Engineering

[Postal Address:  GPO Box U1987, Perth, Western Australia, 6845]   [Bld 613, Rm 409]
[Street Address:  ARRC/CSIRO Building, H Block Level 4, 26 Dick Perry Avenue, Kensington 6151, Western Australia]

Tel     | +61 8 9266 4975
Fax    | +61 8 9266 3407
Email | <email address hidden>
Web   | www.geophysics.curtin.edu.au

Curtin University is a trademark of Curtin University of Technology
CRICOS Provider Code 00301J (WA)

-----Original Message-----
From: <email address hidden> <email address hidden> On Behalf Of Joel Fenwick
Sent: Wednesday, 21 March 2018 3:14 PM
To: Robert Verstandig <email address hidden>
Subject: Re: [Question #666736]: How do I compile escript v5.1 on RHEL 6.9?

Your question #666736 on esys-escript changed:
https://answers.launchpad.net/escript-finley/+question/666736

    Status: Open => Answered

Joel Fenwick proposed the following answer:
I added the following to my options file:

cc_flags = "-std=gnu++0x -pedantic -Wall -fPIC -Wno-unknown-pragmas
-Wno-sign-compare -Wno-system-headers -Wno-long-long -Wno-strict- aliasing -finline-functions"

(It's just the default values with that flag switched.)

I did a build like that and it passed all tests (on my non-RHEL system) so give it a go.

--
If this answers your question, please go to the following page to let us know that it is solved:
https://answers.launchpad.net/escript-finley/+question/666736/+confirm?answer_id=3

If you still need help, you can reply to this email or go to the following page to enter your feedback:
https://answers.launchpad.net/escript-finley/+question/666736

You received this question notification because you asked the question.

Revision history for this message
Robert Vestandig (rverstandig) said : 		#6

Hi Joel

This did not end up working either with v5.1. I was able to get through the compiler checks but there were more errors further on. I was able to install v4.2 so we are now running with that. I guess our OS is not supported and we cannot upgrade to RHEL 7 as we are running legacy apps that are not supported on this platform.

Anyway, I have run out of time on this now but we do have a working solution.

Thanks for your help.

Cheers

Robert W Verstandig  |  Senior Technologist, Exploration Geophysics
Western Australian School of Mines: Minerals, Energy and Chemical Engineering
Faculty of Science and Engineering

[Postal Address:  GPO Box U1987, Perth, Western Australia, 6845]   [Bld 613, Rm 409]
[Street Address:  ARRC/CSIRO Building, H Block Level 4, 26 Dick Perry Avenue, Kensington 6151, Western Australia]

Tel     | +61 8 9266 4975
Fax    | +61 8 9266 3407
Email | <email address hidden>
Web   | www.geophysics.curtin.edu.au

Curtin University is a trademark of Curtin University of Technology
CRICOS Provider Code 00301J (WA)

-----Original Message-----
From: <email address hidden> <email address hidden> On Behalf Of Joel Fenwick
Sent: Wednesday, 21 March 2018 3:14 PM
To: Robert Verstandig <email address hidden>
Subject: Re: [Question #666736]: How do I compile escript v5.1 on RHEL 6.9?

Your question #666736 on esys-escript changed:
https://answers.launchpad.net/escript-finley/+question/666736

    Status: Open => Answered

Joel Fenwick proposed the following answer:
I added the following to my options file:

cc_flags = "-std=gnu++0x -pedantic -Wall -fPIC -Wno-unknown-pragmas
-Wno-sign-compare -Wno-system-headers -Wno-long-long -Wno-strict- aliasing -finline-functions"

(It's just the default values with that flag switched.)

I did a build like that and it passed all tests (on my non-RHEL system) so give it a go.

--
If this answers your question, please go to the following page to let us know that it is solved:
https://answers.launchpad.net/escript-finley/+question/666736/+confirm?answer_id=3

If you still need help, you can reply to this email or go to the following page to enter your feedback:
https://answers.launchpad.net/escript-finley/+question/666736

You received this question notification because you asked the question.

Revision history for this message
Launchpad Janitor (janitor) said : 		#7

This question was expired because it remained in the 'Open' state without activity for the last 15 days.